DOCSLIB.ORG

Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia RESEARCH ARTICLE Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia Sara De Fanti1☯, Chiara Barbieri1☯¤*, Stefania Sarno1, Federica Sevini2,3, Dario Vianello2,3, Erika Tamm4,5, Ene Metspalu4,5, Mannis van Oven4,6, Alexander Hübner7, Marco Sazzini1, Claudio Franceschi2,3,8,9, Davide Pettener1, Donata Luiselli1* 1 Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy, 2 Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy, 3 C.I.G. Interdepartmental Centre L. Galvani for Integrated Studies on Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy, 4 Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia, 5 Department of Evolutionary Biology, University of Tartu, Tartu, Estonia, 6 Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands, 7 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 8 IRCCS, Institute of Neurological Sciences of Bologna, Ospedale Bellaria, Bologna, Italy, 9 CNR, Institute of Organic Synthesis and Photoreactivity (ISOF), Bologna, Italy OPEN ACCESS ☯ These authors contributed equally to this work. ¤ Current Address: Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Citation: De Fanti S, Barbieri C, Sarno S, Sevini F, Human History, Jena, Germany Vianello D, Tamm E, et al. (2015) Fine Dissection of * [email protected] (CB); [email protected] (DL) Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia. PLoS ONE 10(12): e0144391. doi:10.1371/ journal.pone.0144391 Abstract Editor: Ron Pinhasi, University College Dublin, Genetic signatures from the Paleolithic inhabitants of Eurasia can be traced from the early IRELAND divergent mitochondrial DNA lineages still present in contemporary human populations. Received: April 15, 2015 Previous studies already suggested a pre-Neolithic diffusion of mitochondrial haplogroup Accepted: November 17, 2015 HV*(xH,V) lineages, a relatively rare class of mtDNA types that includes parallel branches Published: December 7, 2015 mainly distributed across Europe and West Asia with a certain degree of structure. Up till now, variation within haplogroup HV was addressed mainly by analyzing sequence data Copyright: © 2015 De Fanti et al. This is an open access article distributed under the terms of the from the mtDNA control region, except for specific sub-branches, such as HV4 or the widely Creative Commons Attribution License, which permits distributed haplogroups H and V. In this study, we present a revised HV topology based on unrestricted use, distribution, and reproduction in any full mtDNA genome data, and we include a comprehensive dataset consisting of 316 com- medium, provided the original author and source are credited. plete mtDNA sequences including 60 new samples from the Italian peninsula, a previously underrepresented geographic area. We highlight points of instability in the particular topol- Data Availability Statement: All the newly generated 55 sequences are available in GenBank ogy of this haplogroup, reconstructed with BEAST-generated trees and networks. We also (http://www.ncbi.nlm.nih.gov/genbank/) with confirm a major lineage expansion that probably followed the Late Glacial Maximum and accession codes KP340126-KP340180. preceded Neolithic population movements. We finally observe that Italy harbors a reservoir Funding: This work was supported by the PRIN of mtDNA diversity, with deep-rooting HV lineages often related to sequences present in the Progetti di Ricerca di Interesse Nazionale Caucasus and the Middle East. The resulting hypothesis of a glacial refugium in Southern 2010EL8TXP_006 grant to DL, http://prin.miur.it/; the Italy has implications for the understanding of late Paleolithic population movements and is European Research Council ERC-2011-AdG 295733 (Langelin) to DP and CB, http://erc.europa.eu/; the discussed within the archaeological cultural shifts occurred over the entire continent. Institutional Research Funding from the Estonian Research Council [IUT24-1], http://www.etag.ee/en/ estonian-research-council/; and by the European PLOS ONE | DOI:10.1371/journal.pone.0144391 December 7, 2015 1/19 Fine Dissection of Human Mitochondrial DNA Haplogroup HV Regional Development Fund (European Union), Introduction http://ec.europa.eu/regional_policy/index.cfm/en/ funding/erdf/, through the Centre of Excellence in In the past years, an increasing number of studies reported whole mitochondrial genome data Genomics to Estonian Biocentre and University of from various human populations from all the continents, providing new insights into the Tartu, http://genomics.ebc.ee/. MvO was supported in shape of the matrilineal phylogeny and the distribution of its clades. These fine-grained studies part by an Estonian Biocentre EBC ECOGENE helped to both understand demic migration flows and disentangle the phylogeographic distri- student fellowship, https://edukad.etag.ee/project/ bution and the time of divergence of characteristic mitochondrial DNA (mtDNA) lineages [1– 3010. The funders had no role in study design, data collection and analysis, decision to publish, or 8]. Uniparental genetic markers (i.e. mtDNA and the non-recombinant portion of the Y chro- preparation of the manuscript. mosome) have been widely studied for reconstructing the prehistory of European and Mediter- ranean populations from living individuals [9–13], as well as from ancient DNA (aDNA) Competing Interests: The authors have declared that no competing interests exist. samples [13]. Accordingly, the available published data from these regions provide an extensive geographical coverage, even though at a shallow level of phylogenetic resolution. In fact, until a couple of years ago, population-level analyses of mtDNA focused almost exclusively on the hypervariable segment(s) (HVS) located within the D-loop or control region. Only recently, this kind of studies began to include full mtDNA genome data to explore the variability of spe- cific lineages at a higher resolution and to get deeper insights into the matrilineal prehistory of a given population [5, 14–16]. A recent comprehensive survey of the Italian uniparental genetic landscape, comprising almost a thousand of individuals, revealed that mtDNA haplogroup HV is the lineage in Italy with the oldest coalescence, and highlighted a divergent structure between the Northern and the Southern regions of the peninsula [17]. This early signal can be paralleled with noticeable findings obtained by aDNA analysis on remains from a Mesolithic site in Sicily (Favignana, 14 kilo years ago, kya) [18]), which included a specimen assigned to haplogroup HV1. A Paleo- lithic site in Puglia (Paglicci, 28 kya) also reported data from an individual assigned to HVÃ (or pre-HV/R0) [19], but such finding could not be replicated in a more recent study [20]. While haplogroup HV was recognized as a crucial component of early human dispersal in Eurasia [9,21], patterns of its internal variability have been poorly investigated in previous works, which only focused on the major clades HV4 [4], V and H [21–27]. Haplogroup HV is a major mitochondrial clade within haplogroup R0 [9] characterized by the T14766C mutation and comprising at least 18 recognized basal subclades. Seventeen of these are designated with a consecutive numerical label, i.e. HV0-HV17 (the HV3 label is not used) (http://www.phylotree.org/, Build 16) [28]. Additionally, it includes haplogroup H as one of its direct subclades, while haplogroup V is a nested subhaplogroup within the HV0 clade. The basal structure of the HV phylogeny is partially characterized by mutations located within the hypervariable segments. Some of these branch-defining variants occur for example at nucleotide positions 72, 73, 152, 195, 16311, which are recognized as recurrent sites throughout the whole mtDNA phylogeny—the latter three for example, appears more than 80 times in the tree [29]—and could therefore obscure the topology of the reconstructed HV tree. The HV clade as a whole, including its H subclade, encompasses Eurasian haplogroups that likely arose between Western and Central Asia [30]. Haplogroup HVÃ(xH,V) (i.e. the whole of HV excluding its subclades H and V) is not particularly common in Europe, with frequencies that range between 0% and 10%. In particular, high HVÃ occurrences are observed in Southern Europe (e.g., Italy and Spain) and exceptionally high frequencies are found in Iran (19–24%) [31], although somewhat lower values (9–14%) are reported for the same populations in Farjadian et al. [32]. An average frequency of 4.05% is observed in the Italian peninsula [17]. On the other hand, the major HV subclade, haplogroup H, experienced a vast diffusion during the late Neolithic time, becoming the most common haplogroup in Europe today [27,33].Otherlineageswithinhap- logroup HV were likely spread in more ancient times, dating back to more than 15 kya and having independent diffusions within Europe of Early, Middle or Late Upper Paleolithic origins [9,21]. PLOS ONE | DOI:10.1371/journal.pone.0144391 December 7, 2015 2/19 Fine Dissection of Human Mitochondrial DNA Haplogroup HV Several scholars associated the diffusion of Paleolithic characteristic lineages with the re- peopling
Load more

Recommended publications
  • Ancient Mitochondrial DNA from Pre-Historic
    Grand Valley State University ScholarWorks@GVSU Masters Theses Graduate Research and Creative Practice 4-30-2011 Ancient Mitochondrial DNA From Pre-historic Southeastern Europe: The rP esence of East Eurasian Haplogroups Provides Evidence of Interactions with South Siberians Across the Central Asian Steppe Belt Jeremy R. Newton Grand Valley State University Follow this and additional works at: http://scholarworks.gvsu.edu/theses Part of the Cell Biology Commons, and the Molecular Biology Commons Recommended Citation Newton, Jeremy R., "Ancient Mitochondrial DNA From Pre-historic Southeastern Europe: The rP esence of East Eurasian Haplogroups Provides Evidence of Interactions with South Siberians Across the Central Asian Steppe Belt" (2011). Masters Theses. 5. http://scholarworks.gvsu.edu/theses/5 This Thesis is brought to you for free and open access by the Graduate Research and Creative Practice at ScholarWorks@GVSU. It has been accepted for inclusion in Masters Theses by an authorized administrator of ScholarWorks@GVSU. For more information, please contact [email protected]. ANCIENT MITOCHONDRIAL DNA FROM PRE-HISTORIC SOUTH- EASTERN EUROPE: THE PRESENCE OF EAST EURASIAN HAPLOGROUPS PROVIDES EVIDENCE OF INTERACTIONS WITH SOUTH SIBERIANS ACROSS THE CENTRAL ASIAN STEPPE BELT A thesis submittal in partial fulfillment of the requirements for the degree of Master of Science By Jeremy R. Newton To Cell and Molecular Biology Department Grand Valley State University Allendale, MI April, 2011 “Not all those who wander are lost.” J.R.R. Tolkien iii ACKNOWLEDGEMENTS I would like to extend my sincerest thanks to every person who has motivated, directed, and encouraged me throughout this thesis project. I especially thank my graduate advisor, Dr.
    [Show full text]
  • Mitochondrial DNA Haplogroups Observed in Iraqi Population
    International Journal of Science and Research (IJSR) ISSN (Online): 2319-7064 Index Copernicus Value (2013): 6.14 | Impact Factor (2014): 5.611 Mitochondrial DNA Haplogroups Observed in Iraqi Population Nihad A.M. Al-Rashedi1, Mohammed A. Jebor2, Talib AH Mousa3, Ali H. Al-Saadi4 1, 3 Science College- Muthanna University; 2, 4Science Colleges- Babylon University Abstract: Mitochondrial DNA hypervariable regions I and II of control region were sequenced from 100 random healthy unrelated individuals of three sequential generations belong to the Arab ethnic of Iraqi population. The aim of this study was to detection the mtDNA haplotypes and classifying it into mtDNA haplogroups will be useful in forensic genetics applications and determining the Iraqi population history. The sequence variation within D-loop control region were analyzed the composition of haplogroups that showed high frequency of haplogroups U, H, J,M, D,T and N (18%, 14%,10%, 9%, 7%, 7% and 7%, respectively, moderate frequency of haplogroups L and I was (4%) and B, A, R and K (2%), and low frequency of haplogroup pre-HV (1%) . This study was indicated lack of V, P, Y, X, O, Z, Q, G, E and C haplogroups. Keywords: mitochondrial DNA, haplogroups, DNA Sequencing, Arabic Iraqi population 1. Introduction find it http://mtmanager.yonsei.ac.kr that enables automatically estimate the most mtDNA haplogroups Iraq is located in the Middle East which bordered by Saudi according to control‐region mutation variations and scanning Arabia, Iran, Jordan, Kuwait and Turkey. The Iraqi of similar sequences from the database which includes over population consists of 75–80% Arabs and 20-25% others.
    [Show full text]
  • Rare Human Mitochondrial HV Lineages Spread from the Near East
    www.nature.com/scientificreports OPEN Rare human mitochondrial HV lineages spread from the Near East and Caucasus during post-LGM and Received: 11 January 2019 Accepted: 21 June 2019 Neolithic expansions Published: xx xx xxxx Michel Shamoon-Pour1, Mian Li2 & D. Andrew Merriwether1 Of particular signifcance to human population history in Eurasia are the migratory events that connected the Near East to Europe after the Last Glacial Maximum (LGM). Utilizing 315 HV*(xH,V) mitogenomes, including 27 contemporary lineages frst reported here, we found the genetic signatures for distinctive movements out of the Near East and South Caucasus both westward into Europe and eastward into South Asia. The parallel phylogeographies of rare, yet widely distributed HV*(xH,V) subclades reveal a connection between the Italian Peninsula and South Caucasus, resulting from at least two (post-LGM, Neolithic) waves of migration. Many of these subclades originated in a population ancestral to contemporary Armenians and Assyrians. One such subclade, HV1b-152, supports a postexilic, northern Mesopotamian origin for the Ashkenazi HV1b2 lineages. In agreement with ancient DNA fndings, our phylogenetic analysis of HV12 and HV14, the two exclusively Asian subclades of HV*(xH,V), point to the migration of lineages originating in Iran to South Asia before and during the Neolithic period. With HV12 being one of the oldest HV subclades, our results support an origin of HV haplogroup in the region defned by Western Iran, Mesopotamia, and the South Caucasus, where the highest prevalence of HV has been found. Te major subclade of R0, haplogroup HV has a pivotal position in human mitochondrial (mtDNA) phylogeny as the ancestral clade to haplogroup H-the most common clade in Europe1 and the best-defned mtDNA hap- logroup according to Phylotree2.
    [Show full text]
  • Western Eurasian Ancestry in Modern Siberians Based on Mitogenomic Data
    Derenko et al. BMC Evolutionary Biology 2014, 14:217 http://www.biomedcentral.com/1471-2148/14/217 RESEARCH ARTICLE Open Access Western Eurasian ancestry in modern Siberians based on mitogenomic data Miroslava Derenko1*, Boris Malyarchuk1, Galina Denisova1, Maria Perkova1, Andrey Litvinov1, Tomasz Grzybowski2, Irina Dambueva3, Katarzyna Skonieczna2, Urszula Rogalla2, Iosif Tsybovsky4 and Ilya Zakharov5 Abstract Background: Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected previously in mitochondrial gene pools of modern Siberians. Results: We report here 166 new complete mitochondrial DNA (mtDNA) sequences that allow us to expand and re-analyze the available data sets of western Eurasian lineages found in northern Asian populations, define the phylogenetic status of Siberian-specific subclades and search for links between mtDNA haplotypes/subclades and events of human migrations. From a survey of 158 western Eurasian mtDNA genomes found in Siberia we estimate that nearly 40% of them most likely have western Asian and another 29% European ancestry. It is striking that 65 of northern Asian mitogenomes, i.e. ~41%, fall into 19 branches and subclades which can be considered as Siberian-specific being found so far only in Siberian populations. From the coalescence analysis it is evident that the sequence divergence of Siberian-specific subclades was relatively small, corresponding to only 0.6-9.5 kya (using the complete mtDNA rate) and 1–6kya(codingregionrate).
    [Show full text]
  • Ancient Human Mitochondrial Genomes from Bronze Age
    www.nature.com/scientificreports OPEN Ancient human mitochondrial genomes from Bronze Age Bulgaria: new insights into the Received: 26 July 2018 Accepted: 20 March 2019 genetic history of Thracians Published: xx xx xxxx Alessandra Modi1, Desislava Nesheva2, Stefania Sarno3, Stefania Vai 1, Sena Karachanak- Yankova2, Donata Luiselli4, Elena Pilli1, Martina Lari1, Chiara Vergata1, Yordan Yordanov5, Diana Dimitrova6, Petar Kalcev7, Rada Staneva2, Olga Antonova2, Savina Hadjidekova2, Angel Galabov8, Draga Toncheva2 & David Caramelli1 One of the best documented Indo-European civilizations that inhabited Bulgaria is the Thracians, who lasted for more than fve millennia and whose origin and relationships with other past and present- day populations are debated among researchers. Here we report 25 new complete mitochondrial genomes of ancient individuals coming from three necropolises located in diferent regions of Bulgaria – Shekerdja mogila, Gabrova mogila and Bereketska mogila – dated to II-III millennium BC. The identifed mtDNA haplogroup composition refects the mitochondrial variability of Western Eurasia. In particular, within the ancient Eurasian genetic landscape, Thracians locate in an intermediate position between Early Neolithic farmers and Late Neolithic-Bronze Age steppe pastoralists, supporting the scenario that the Balkan region has been a link between Eastern Europe and the Mediterranean since the prehistoric time. Spatial Principal Component Analysis (sPCA) performed on Thracian and modern mtDNA sequences, confrms the pattern highlighted on ancient populations, overall indicating that the maternal gene pool of Thracians refects their central geographical position at the gateway of Europe. Bulgaria is situated in the eastern part of the Balkan Peninsula, at the connection point between Southeastern Europe, Eurasian steppe, Anatolia and the Aegean islands.
    [Show full text]
  • Haplogroup I1 (Y-DNA) Facts About Genetics Y-DNA Haplogroups Haplogroup E1b1b Haplogroup G2a
    3/13/2016 10:11 AM http://www.eupedia.com/europe/Haplogroup_I1_Y-DNA.shtml DNA Tutorials Eupedia Home > Genetics > Haplogroups (home) > Haplogroup I1 Video Tutorials @ DNA Haplogroup I1 (Y-DNA) Facts about Genetics Y-DNA haplogroups Haplogroup E1b1b Haplogroup G2a Haplogroup I1 Haplogroup I2 Haplogroup J1 Haplogroup J2 Contents Haplogroup N1c Haplogroup Q 1. Geographic distribution Author: Maciamo Haplogroup R1a Last update February 2015 (updated phylogeny). Haplogroup R1b 2. Origins & History Haplogroup T 2.1 How did I1 become Nordic? Famous Y-DNA 2.2 How did I1 become Germanic? Y-DNA by country 2.3 I1 in Finland 2.4 Germanic migrations Y-DNA Maps MtDNA haplogroups 3. Subclades & Haplotypes Haplogroup H 3.1 Grouping by STR Haplogroup HV 3.2 SNP Analysis Haplogroup I 4. Famous I1 individuals Haplogroup J Haplogroup K Haplogroup T Haplogroup U2 Haplogroup U3 Haplogroup U4 Geographic distribution Haplogroup U5 Haplogroup U6 Haplogroup I1 is the most common I subclade in northern Europe. It is found mostly in Scandinavia and Finland, where it typically represent over 35% of the male Y-chromosomes. Associated with the Norse ethnicity, I1 is found in all places Haplogroup V invaded by ancient Germanic tribes and the Vikings. Other parts of Europe speaking Germanic languages come next in Haplogroup W frequency. Germany, Austria, the Low Countries, England and the Scottish Lowlands all have between 10% and 20% of I1 Haplogroup X lineages. MtDNA by country Distribution of haplogroup I1 in Europe MtDNA Maps Diseases linked to mtDNA Regional history
    [Show full text]
  • The Population History of the Croatian Linguistic Minority of Molise (Southern Italy): a Maternal View
    European Journal of Human Genetics (2005) 13, 902–912 & 2005 Nature Publishing Group All rights reserved 1018-4813/05 $30.00 www.nature.com/ejhg ARTICLE The population history of the Croatian linguistic minority of Molise (southern Italy): a maternal view Carla Babalini1,5, Cristina Martı´nez-Labarga1,5, Helle-Viivi Tolk2, Toomas Kivisild2, Rita Giampaolo1, Tiziana Tarsi1, Irene Contini1, Lovorka Barac´3, Branka Janic´ijevic´3, Irena Martinovic´ Klaric´3, Marijana Pericˇic´3, Anita Sujoldzˇic´3, Richard Villems2, Gianfranco Biondi4, Pavao Rudan3 and Olga Rickards*,1 1Department of Biology, University of Rome ‘Tor Vergata’, 00133 Rome, Italy; 2Department of Evolutionary Biology, University of Tartu, and Estonian Biocentre, 51010 Tartu, Estonia; 3Institute for Anthropological Research, 10000 Zagreb, Croatia; 4Department of Environmental Sciences, University of L’Aquila, 67010 L’Aquila, Italy This study examines the mitochondrial DNA (mtDNA) diversity of the Croatian-speaking minority of Molise and evaluates its potential genetic relatedness to the neighbouring Italian groups and the Croatian parental population. Intermatch, genetic distance, and admixture analyses highlighted the genetic similarity between the Croatians of Molise and the neighbouring Italian populations and demonstrated that the Croatian-Italian ethnic minority presents features lying between Croatians and Italians. This finding was confirmed by a phylogeographic approach, which revealed both the prevalence of Croatian and the penetrance of Italian maternal lineages in the Croatian community of Molise. These results suggest that there was no reproductive isolation between the two geographically proximate, yet culturally distinct populations living in Italy. The gene flow between the Croatian-Italians and the surrounding Italian populations indicate, therefore, that ethnic consciousness has not created reproductive barriers and that the Croatian-speaking minority of Molise does not represent a reproductively isolated entity.
    [Show full text]
  • Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata
    University of Pennsylvania ScholarlyCommons Department of Anthropology Papers Department of Anthropology 5-29-2013 Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata Alessio Boattini Begoña Martinez-Cruz Stefania Sarno Christine Harmant Antonella Useli See next page for additional authors Follow this and additional works at: https://repository.upenn.edu/anthro_papers Part of the Anthropology Commons, and the Genetics and Genomics Commons Recommended Citation Boattini, A., Martinez-Cruz, B., Sarno, S., Harmant, C., Useli, A., Sanz, P., Yang-Yao, D., Manry, J., Ciani, G., Luiselli, D., Quintana-Murci, L., Comas, D., Pettener, D., Genographic Consortium, & Schurr, T. G. (2013). Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata. PLoS ONE, 8 (5), e65441. https://doi.org/10.1371/journal.pone.0065441 Theodore G. Schurr is not listed as an individual author on this paper but is part of the Genographic Consortium. A full list of Genographic Consortium members for this paper can be found in the Acknowledgements. This paper is posted at ScholarlyCommons. https://repository.upenn.edu/anthro_papers/41 For more information, please contact [email protected]. Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata Abstract Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure.
    [Show full text]
  • Massively Parallel Sequencing of Human Mitochondrial Genome for Forensic Analysis
    TALLINN UNIVERSITY OF TECHNOLOGY DOCTORAL THESIS 15/2020 Massively Parallel Sequencing of Human Mitochondrial Genome for Forensic Analysis MONIKA STOLJAROVA TALLINN UNIVERSITY OF TECHNOLOGY School of Science Department of Chemistry and Biotechnology This dissertation was accepted for the defence of the degree 19/05/2020 Supervisor: Dr. Anu Aaspõllu Department of Chemistry and Biotechnology Tallinn University of Technology Tallinn, Estonia Co-supervisor: Dr. Bruce Budowle Center for Human Identification University of North Texas Health Science Center Fort Worth, TX, USA Opponents: Prof Ángel Carracedo Álvarez Institute of Forensic Sciences University of Santiago de Compostela Santiago de Compostela, Galicia, Spain Prof Mait Metspalu Institute of Genomics University of Tartu Tartu, Estonia Defence of the thesis: 22/06/2020, Tallinn Declaration: Hereby I declare that this doctoral thesis, my original investigation and achievement, submitted for the doctoral degree at Tallinn University of Technology has not been submitted for doctoral or equivalent academic degree. Monika Stoljarova signature Copyright: Monika Stoljarova, 2020 ISSN 2585-6898 (publication) ISBN 978-9949-83-552-2 (publication) ISSN 2585-6901 (PDF) ISBN 978-9949-83-553-9 (PDF) TALLINNA TEHNIKAÜLIKOOL DOKTORITÖÖ 15/2020 Inimese mitokondriaalse genoomi massiivselt paralleelne sekveneerimine forensiliseks analüüsiks MONIKA STOLJAROVA Contents List of Publications ............................................................................................................ 6 Author’s
    [Show full text]
  • Mitochondrial DNA Haplogroups and Breast Cancer Risk Factors in the Avon Longitudinal Study of Parents and Children (ALSPAC)
    G C A T T A C G G C A T genes Article Mitochondrial DNA Haplogroups and Breast Cancer Risk Factors in the Avon Longitudinal Study of Parents and Children (ALSPAC) Vivienne Riley 1, A Mesut Erzurumluoglu 2,3 ID , Santiago Rodriguez 3 ID and Carolina Bonilla 3,4,5,* ID 1 MSc Genomic Medicine Programme, G7, College House, St Luke’s Campus University of Exeter, Exeter, Devon EX2 4TE, UK; [email protected] 2 Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK; [email protected] 3 MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; [email protected] 4 Integrative Cancer Epidemiology Program, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK 5 Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil * Correspondence: [email protected] Received: 9 June 2018; Accepted: 27 July 2018; Published: 1 August 2018 Abstract: The relationship between mitochondrial DNA (mtDNA) and breast cancer has been frequently examined, particularly in European populations. However, studies reporting associations between mtDNA haplogroups and breast cancer risk have had a few shortcomings including small sample sizes, failure to account for population stratification and performing inadequate statistical tests. In this study we investigated the association of mtDNA haplogroups of European origin with several breast cancer risk factors in mothers and children of the Avon Longitudinal Study of Parents and Children (ALSPAC), a birth cohort that enrolled over 14,000 pregnant women in the Southwest region of the UK.
    [Show full text]
  • Evidence for Discontinuity Between Prehistoric and Modern Europeans
    Journal of Genetic Genealogy 1:40-50, 2005 We Are Not Our Ancestors: Evidence for Discontinuity between Prehistoric and Modern Europeans Ellen Levy-Coffman The model of European genetic ancestry has recently shifted away from the Neolithic diffusion model towards an emphasis on autochthonous Paleolithic origins. However, this new paradigm utilizes genetic reconstructions based primarily on contemporary populations and, furthermore, is often promoted without regard to the findings of ancient DNA studies. These ancient DNA studies indicate that contemporary European ancestry is not a living fossil of the Paleolithic maternal deme; rather, demographic events during the Neolithic and post-Neolithic periods appear to have had substantial impact on the European genetic record. In addition, evolutionary processes, including genetic drift, adaptive selection and disease susceptibility, may have altered the patterns of maternal lineage frequency and distribution in existing populations. As a result, the genetic history of Europe has undergone significant transformation over time, resulting in genetic discontinuity between modern-day Europeans and their ancient maternal forbearers. Introduction Thus, the picture presented by this model is one of substantial genetic continuity between modern groups The genetic model currently presented by many and the Paleolithic hunter-gatherers who inhabited the population geneticists emphasizes the autochthonous same region thousands of years ago. Paleolithic ancestry of contemporary Europeans. This paradigm is based on the perspective that contemporary Yet the DNA evidence suggests a more complex picture Europeans descend primarily from their hunter-gatherer than a direct and undisturbed genetic link between forbearers who lived in the same region until contemporary Europeans and their Paleolithic approximately 10,000 years ago, when the beginning of forbearers.
    [Show full text]
  • Two-Stage Association Study and Meta-Analysis of Mitochondrial DNA Variants in Parkinson Disease
    Two-stage association study and meta-analysis of mitochondrial DNA variants in Parkinson disease Gavin Hudson, PhD ABSTRACT Mike Nalls, PhD Objectives: Previous associations between mitochondrial DNA (mtDNA) and idiopathic Parkinson Jonathan R. Evans, disease (PD) have been inconsistent and contradictory. Our aim was to resolve these inconsisten- MRCP, PhD cies and determine whether mtDNA has a significant role in the risk of developing PD. David P. Breen, MRCP Methods: Two-stage genetic association study of 138 common mtDNA variants in 3,074 PD Sophie Winder-Rhodes, cases and 5,659 ethnically matched controls followed by meta-analysis of 6,140 PD cases BSc and 13,280 controls. Karen E. Morrison, MD . Huw R. Morris, MRCP, Results: In the association study, m.2158T C and m.11251A Gwereassociatedwitha PhD reduced risk of PD in both the discovery and replication cohorts. None of the common European Caroline H. Williams- mtDNA haplogroups were consistently associated with PD, but pooling of discovery and replica- “ ” Gray, MCRP, PhD tion cohorts revealed a protective association with super-haplogroup JT. In the meta-analysis, Roger A. Barker, MCRP, there was a reduced risk of PD with haplogroups J, K, and T and super-haplogroup JT, and an PhD increase in the risk of PD with super-haplogroup H. Andrew B. Singleton, Conclusions: In a 2-stage association study of mtDNA variants and PD, we confirm the reduced PhD risk of PD with super-haplogroup JT and resolve this at the J1b level. Meta-analysis explains John Hardy, MD, PhD the previous inconsistent associations that likely arise through sampling effects.
    [Show full text]